Software | Name | Version | Classification |
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XDS | | data reductionPHASER | 2.5.1phasingPHENIX | | refinementPDB_EXTRACT | 3.15 | data extractionSCALA | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1jri Resolution: 2.6→49.303 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: TWIN_LSQ_F
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1775 | 878 | 5.07 % |
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Rwork | 0.1409 | 16430 | - |
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obs | 0.1442 | 17319 | 99.99 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso max: 175.17 Å2 / Biso mean: 55.0035 Å2 / Biso min: 24.48 Å2 |
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Refinement step | Cycle: final / Resolution: 2.6→49.303 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4334 | 0 | 0 | 50 | 4384 |
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Biso mean | - | - | - | 48.08 | - |
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Num. residues | - | - | - | - | 552 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 4369 | X-RAY DIFFRACTION | f_angle_d1.091 | 5885 | X-RAY DIFFRACTION | f_chiral_restr0.039 | 716 | X-RAY DIFFRACTION | f_plane_restr0.005 | 744 | X-RAY DIFFRACTION | f_dihedral_angle_d15.464 | 1700 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.6003-2.7631 | 0.3253 | 164 | 0.2598 | 2699 | 2863 | 94 | 2.7631-2.9762 | 0.2498 | 145 | 0.2165 | 2773 | 2918 | 95 | 2.9762-3.2753 | 0.2079 | 148 | 0.1771 | 2735 | 2883 | 95 | 3.2753-3.7483 | 0.1683 | 138 | 0.1514 | 2724 | 2862 | 95 | 3.7483-4.719 | 0.1518 | 142 | 0.1128 | 2749 | 2891 | 95 | 4.719-28.4671 | 0.1433 | 141 | 0.112 | 2750 | 2891 | 95 |
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Refinement TLS params. | Method: refined / Origin x: 134.3083 Å / Origin y: 148.0233 Å / Origin z: 95.0828 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.3982 Å2 | -0.0295 Å2 | 0.0455 Å2 | - | 0.3251 Å2 | 0.1046 Å2 | - | - | 0.1619 Å2 |
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L | 2.1943 °2 | -0.1531 °2 | 0.2541 °2 | - | 0.8179 °2 | 0.7661 °2 | - | - | 0.2909 °2 |
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S | -0.0622 Å ° | -0.0117 Å ° | -0.0237 Å ° | -0.02 Å ° | 0.0077 Å ° | -0.034 Å ° | -0.0241 Å ° | -0.0814 Å ° | 0.0577 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | allA7 - 84 | 2 | X-RAY DIFFRACTION | 1 | allB6 - 82 | 3 | X-RAY DIFFRACTION | 1 | allC6 - 82 | 4 | X-RAY DIFFRACTION | 1 | allD4 - 82 | 5 | X-RAY DIFFRACTION | 1 | allE6 - 82 | 6 | X-RAY DIFFRACTION | 1 | allF5 - 87 | 7 | X-RAY DIFFRACTION | 1 | allG5 - 85 | 8 | X-RAY DIFFRACTION | 1 | allS2 - 78 | | | | | | | | | | | | | | | | |
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